Once a Murderer, Now a Hero 2: Guilty
by 9tailedfox657
Summary: 5 years have past since Naruto and Itachi returned to the Leaf Village. 5 years of training with Kakashi, Jiraiya, and Sasuke have trained the duo for a threat greater than any they have seen. However now they return to the Leaf with a new mission and with a new group of allies and enemies. What evils await Naruto and the Leaf Village? Rated T for now but could change later.
1. Prologue

Once a Murderer, Now a Hero 2: _Guilty_

Prologue: 

The Deceptive Shadows

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_A fact is a simple statement that everyone believes. It is innocent, unless found guilty. A hypothesis is a novel suggestion that no one wants to believe. It is guilty, until found effective.__ – Edward Teller_

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In a place hidden from the entire ninja world a man enters a cave concealed from the eyes of any man, woman or shinobi…

"It appears that the Leaf Village is gathering their forces for something. Do you think they found out about us?" the first man asked.

"I wouldn't worry about it too much. No one will be able to know of our plan. They are most likely increasing the defenses of their great city" the second one said.

"You better hope so because _he _wants this thing to remain quiet until the time comes" the first man said.

"I know what _he _wants. What I need is something greater" the second man said.

"Something greater? What are you talking about?" the first man asked.

"The tests I have been running well…The results have been coming out negative now" the second man said.

"Explain" the first man said.

"Well it's the subjects they seem to have _developed _over the past five years" the second man said.

"Developed?" the first asked.

"Well they seem to have found immunity to the affects of the girl's blood. For some it's just another blood transplant for others it acts like a type of poison for them which inevitably kills them at an alarmingly fast rate" the second one said.

"But you told me-"

"I know what I told you" the second one interrupted "I never expected these dragons to just quickly evolve. It appears we still have a lot of variables to account for. Thankfully we have enough blood to experiment with"

"You better hope so because when he finds out about this he won't be too happy. He just might find a better replacement" the first man said.

The second man laughed maniacally and then said "And who does he expect to find? I am the best there is on this specific matter in fact I am the only one that can do this. No one else will be able to help you with these experiments because none of them contain the bestiary like my family did for generations"

"Which is why, we still trust you. Now you still three years left to figure out all this mess. In three years they will have matured. In three years we will have amassed our army. In three years we will attack the ninja villages" the first man said

"Is that all you came to tell me? Our plan of action because I have known that for years" the second man said.

"Well that isn't all I came to tell you. My boss gave me a couple messages for you" the first man said.

"Of course he did" the second man said.

"He says he has found another Rinnegan user and to be very cautious of him" the first man explained.

"Another one, eh? Well that could complicate things a little bit" the second man said "What else?"

"He was questioning the girl. How can you be sure that she doesn't find out about her powers?" the first man asked.

"Well I can't be sure if she does or does not. But what I can be sure of is that even if she does that poison in her system will react to it. So she will no longer be a threat to us" the second man said.

"Is there a cure for that poison?" the first man asked.

"Only one and only I know about it" the second man said.

"What about her blood? What if after her maturity her blood may have the answers for our little problem?" the first man asked.

"Well then let's just hope she conceives a child before she discovers her powers. After all parents pass their lineage through their children, her child will have the same type of power in its blood as well" the second man said.

"Well let's plan for the worst and hope for the best" the first man said.

"Is that all?" the second man asked.

"Not quite. There is something else…something only you would understand" the first man said. The second man looked at him curiously and asked "What is it?"

The first man smiled and then handed to the second man a folder from within his robes. The second man took it and when he opened its contents his eyes went wide.

"My boss said to consider it a gift that he was able to find that" the first man said.

The second man with a very excited grin waved the folder in front of the first man and then asked "Do you realize that this one folder is going to change everything?"

"Oh, yes I do because I have read that myself on my boss' bequest. It appears this document can change the outcome of our entire ninja war" the first man said.

The second man smiled and looked back excitingly to the folder and then said "Well what are we waiting for we've got work to do…"

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**AN: **Well I guess you know what this means. Yes Naruto is back and so is the story loved by so many of you. I wanted to say that firstly you guys are in for a real treat with this story. Secondly is that I have added some new characters to the story that will have significant impact and no they aren't in this prologue. I will do what I can in terms of updating this story my scheduling has been very off this summer but now I am comfortably vacationing in Munich (much to my girlfriends dismay). I also have to make time for sight seeing and family. Germany is a very beautiful place and I want to shout out to any Germans who read this story "I LOVE YOUR COUNTRY". Anyways please Rate and Review I really want to hear your guys' criticism on this story.


	2. Chapter 1

Chapter 1

The Long Awaited Day

**Five Years Later**

The village was silent. Silent meaning it carried on its normal everyday routine. The villagers continued to live as though there was no threat and all was well. However there was an evil looming that the third Hokage warned them about. Yet the village remains silent as though they think their shinobi's could protect them from any harm. Did they not know what was coming? Sakura asked in her head as she walked down the busy street.

She saw each villager laugh, mourn, praise and complain for their own causes as though life was meant to go on. "Do they not know what dangers they face" she asked herself but she knew the answer. The answer was 'yes' they do know what they face however they choose simply to not believe it. They would rather believe that their life has no threat and that all was well.

"Hopefully all goes well" Sakura said to herself in her head. She walked towards the hospital where she practically spent each of her waking moments. She needed a hobby to do after all her boyfriend and all her friends were all busy doing something. She took private lessons from Tsunade which were private from everyone else. Sakura marveled at how fast she was able to learn from her and continued until she could master pretty much everything Tsunade had known. Tsunade herself marveled at this enough so that she called Sakura her 'protégée.'

Sakura felt proud of herself since that moment. She always found herself useless while her teammates were both considered the best ninja's that the leaf has ever seen. She needed to catch up with them. 5 years training with another sannin paid off wonders. Not only was Sakura able to gain more abilities, she was also able to become a medical ninja along the same caliber as Tsunade.

When she entered to hospital she was a little surprised to find more quiet at this time. Usually most days are hectic and flooded with people. Today was a bit more peaceful which was something the hospital needed.

Sakura walked towards the receptionist who was sitting to her right in her personal desk and then asked "Did Lady Tsunade come in?"

The receptionist smiled and then said "Yeah, she's in her usual spot dear" and then got back to working on her desk. Sakura nodded and then left to the one place Tsunade ever seems to go.

She knocked on the door before she entered. It was a habit her mother always enforced on her. When there was no response she opened the door to find Tsunade sitting beside the patient filling out a chart. As soon as Sakura entered Tsunade gave a warm smile and then said "Morning Sakura"

"Morning, sensei" she said. It was another habit that she developed, calling Tsunade sensei.

"What brings you here?" she asked.

"I thought there could be some work at the hospital but it turns out I was wrong" Sakura said.

"Yeah, I found it strange too that there was nothing going on here as well so I decided to tend to this one" she said while nodding her head to the patient.

"Anything?" Sakura asked.

"No, not yet. His condition is very rare and most likely getting worse each day. I can't even calculate how much time he has left which worries me deeply" Tsunade said as she gazed towards the patient with a sad expression.

"Well then if there is any work you know where to reach me" Sakura said and turned around.

"Wait!" Tsunade called out.

Sakura turned back to her sensei "I need you to do me a favour" Tsunade said.

"What is it?" Sakura asked.

"I need you to deliver this letter to the guards at the front gate and ask them for their night shift reports. That is all" she said. Tsunade held out the letter which Sakura took from her and then went back to working on the chart. Sakura went back out and started heading towards the gate

She kept thinking about the day her boyfriend left and kept wondering which day he will come back. She used to sometimes stand near the gate and just wait there hoping that by some miracle he would just appear there. However he been to training for and important mission, so did the rest of the shinobi's including her and her best friend Ino. Everyday they would be training with almost every teacher until they could master pretty much everything that they knew. After all they were going to go on a life or death mission chasing the seven swordsmen of the mist. All of whom were branded nothing less then S-Class ninja's; well according to rumors.

She reached the front gate and saw the two guards sitting down on the desk discussing something. As she approached them they turned their attention towards her. Sakura smiled and then said "Lady Tsunade has left you guys a letter and she would like your night shift reports" she handed them the letter and they in turn handed her the reports.

"Hey you might want to head back to the village" one of the guards said.

Sakura raised an eyebrow; the other guard gave a playful smile and then said "Trust me you'll find some very old friends there."

Sakura thought long and hard about what they meant and then she finally got it. They both grinned when they saw that she figured it out. Sakura ran towards the village in search of the very person she had waited 5 years for. The very person who would send her letters every week, the very person whom she had loved unquestionably, the very person who acknowledged her and noticed her.

"Naruto" she said out loud while running through the village. She started at the Hokage building but she didn't find anyone there. She then went to the hospital just in case sure. When she got there she saw the figures of Jiraiya, Itachi, Kakashi and another ninja whom she barely recognized but realized that was Sasuke because of the Uchiha symbol showing at the back of his shirt. They were all walking into the hospital but she didn't see any sign of blonde hair anywhere.

Where is he? She asked herself.

She then felt arms sneak around her waist and pulled her towards a warm body which she felt comfortable with.

"Miss me" a voice said from behind her; a very familiar and yet different voice. She turned around to see the one person she was searching for this entire time.

"Naruto…"

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**AN: **Turns out that this has been a long awaited day for more than just one person. I hope you guys liked this chapter cuz believe it or not it was the one that gave me the most trouble. I hope it's long enough for you guys if not I'll try to make some of them a little longer. Considering the sheer size of what I planned ahead for this series I might have to split the series once more. I don't know yet but I will let you guys know. This series will definately have longer chapters, exciting storylines and interesting characters both OOC and ones that I made up for this fan fic. As I have mentioned in the first series this story is going to get darker, very darker. It's going to have a lot of character deaths and tragedy that you guys might just hate me by the end of it. I won't mention any names or anything else the rest is up to you guys to find out in the further chapters. Now I want ask you guys if you want me to do an *intimate scene with Naruto and Sakura, just a heads up i haven't done any yet so choose carefully and please comment your answers. As always Rate and Review please


	3. Chapter 2

**Chapter 2**

**Unknown Location****  
**

"What can you do with this newly discovered info?" the second man asked.

"What I can" the first man replied.

"What's stopping you?" the second man asked.

"I need a lot of research and resources…Resources that lie in many of the villages" the first man replied.

"And that is a problem…how?" the second man asked.

"Some of those resources are highly valued, therefore highly protected. We can't get them ourselves with the various bounties on our heads. It would be very difficult for our moles as well," the first man said.

"My boss said not to worry about resources, especially 'highly valued' ones" the second man said.

"Even, then I would need more stuff in preparation of everything" the first man said.

"What else do you need?" the second man asked.

"A whole list of things but mainly the subject itself" the first man said.

"That might be a little difficult" the second man said.

"But necessary. I need to run various tests so that I can understand the meaning of all this" the first man said while waving the folder "Otherwise I can't help, not unless I know what we are dealing with. I need to know how much power I'm dealing with"

"If you aren't able to get the subject?" the second man asked.

"Well, then I'd be running on guesses and chances are your uh, weapon won't be able to work. It might not be strong enough to contain that sort of power. I need to see it's full potency" the first man replied.

"Okay, but how long will it take to get everything ready?" the second man asked

"If it's something powerful; which I'm assuming it is…It could take maybe a year" the first man replied

"A year!" the second man said, incredulously

"Well considering the scale of what I have to make and the load every working component will face I have to carefully plan every step out. And it has to be flawless, otherwise all this planning, it'll just be for nothing" the first man responded.

"Well then we've got a lot of work to do…Doctor" the second man said.

"Yes, we do", the doctor looked out towards the rainy skies "The ninja world will not be able to stop what's coming for them" he said.

"Agreed" the second man said, looking at the drenched atmosphere "So, where to first" he said.

The doctor looks back to the second man and smirks "Rain village…"

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**AN: **Sorry for the long wait guys. I've had multiple responsibilities and was busy most of the time, now that Christmas is here I have more time to write. Expect another chapter soon.


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